# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 11:10:44 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 1-cyclohexyl-3-(4-iodophenyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Ic1ccc(NC(=O)NC2CCCCC2)cc1
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 CIU  CIU  1-cyclohexyl-3-(4-iodophenyl)urea  ligand  34  17  .  2021-08-07  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CIU
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 CIU  C1    C  CH2   0  -0.437  -0.2505  -0.9989   7.2625
 CIU  C2    C  CH2   0  -0.439   0.5729  -0.9576   5.9790
 CIU  C3    C  CH1   0  -0.053  -0.1587  -0.1903   4.8813
 CIU  C4    C  CH2   0  -0.423  -0.5210   1.2196   5.3497
 CIU  C5    C  CH2   0  -0.440  -1.3434   1.1780   6.6342
 CIU  C6    C  CH2   0  -0.432  -0.6220   0.4038   7.7322
 CIU  N1    N  NH1   0  -0.689   0.6423  -0.1762   3.6734
 CIU  C7    C  C     0   0.742   0.1040  -0.1996   2.4338
 CIU  O2    O  O     0  -0.521  -1.0936  -0.3254   2.2213
 CIU  N2    N  NH1   0  -0.792   1.0397  -0.0899   1.4278
 CIU  C8    C  CR6   0   0.381   0.8262  -0.0833   0.0558
 CIU  C9    C  CR16  0  -0.308  -0.3573  -0.4877  -0.5677
 CIU  C10   C  CR16  0  -0.212  -0.4624  -0.4638  -1.9516
 CIU  C11   C  CR6   0  -0.246   0.6040  -0.0461  -2.7307
 CIU  C12   C  CR16  0  -0.212   1.7896   0.3507  -2.1289
 CIU  C13   C  CR16  0  -0.345   1.8922   0.3324  -0.7496
 CIU  HC11  H  HCH2  0   0.214  -1.1633  -1.5786   7.0881
 CIU  HC12  H  HCH2  0   0.233   0.3057  -1.5269   8.0402
 CIU  HC21  H  HCH2  0   0.239   0.7964  -1.9696   5.6329
 CIU  HC22  H  HCH2  0   0.216   1.5347  -0.4716   6.1826
 CIU  HC31  H  HCH1  0   0.236  -1.0830  -0.7254   4.6486
 CIU  HC41  H  HCH2  0   0.211   0.4013   1.7870   5.5183
 CIU  HC42  H  HCH2  0   0.234  -1.0718   1.7378   4.5608
 CIU  HC51  H  HCH2  0   0.213  -2.3081   0.7009   6.4291
 CIU  HC52  H  HCH2  0   0.232  -1.5670   2.1938   6.9677
 CIU  HC61  H  HCH2  0   0.230  -1.2450   0.3487   8.6281
 CIU  HC62  H  HCH2  0   0.211   0.2878   0.9428   8.0182
 CIU  HN1   H  HNH1  0   0.392   1.6256   0.0185   3.7835
 CIU  HN2   H  HNH1  0   0.409   1.9931   0.0862   1.7062
 CIU  H9    H  HCR6  0   0.285  -1.2018  -0.8281   0.0075
 CIU  H10   H  HCR6  0   0.277  -1.3913  -0.7847  -2.4035
 CIU  H12   H  HCR6  0   0.279   2.6370   0.6801  -2.7145
 CIU  H13   H  HCR6  0   0.277   2.8207   0.6520  -0.2913
 CIU  I4    I  I     0   0.039   0.4286  -0.0171  -4.8261

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 CIU  C1   C2    single    1.525  0.020  1.525
 CIU  C1   C6    single    1.525  0.020  1.525
 CIU  C1   HC11  single    0.970  0.020  1.090
 CIU  C1   HC12  single    0.970  0.020  1.090
 CIU  C2   C3    single    1.526  0.020  1.526
 CIU  C2   HC21  single    0.970  0.020  1.090
 CIU  C2   HC22  single    0.970  0.020  1.090
 CIU  C3   C4    single    1.529  0.020  1.529
 CIU  C3   N1    single    1.449  0.020  1.449
 CIU  C3   HC31  single    0.970  0.020  1.090
 CIU  C4   C5    single    1.526  0.020  1.526
 CIU  C4   HC41  single    0.970  0.020  1.090
 CIU  C4   HC42  single    0.970  0.020  1.090
 CIU  C5   C6    single    1.525  0.020  1.525
 CIU  C5   HC51  single    0.970  0.020  1.090
 CIU  C5   HC52  single    0.970  0.020  1.090
 CIU  C6   HC61  single    0.970  0.020  1.090
 CIU  C6   HC62  single    0.970  0.020  1.090
 CIU  N1   C7    single    1.352  0.020  1.352
 CIU  N1   HN1   single    0.860  0.020  1.020
 CIU  C7   O2    double    1.223  0.020  1.223
 CIU  C7   N2    single    1.378  0.020  1.378
 CIU  N2   C8    single    1.389  0.020  1.389
 CIU  N2   HN2   single    0.860  0.020  1.020
 CIU  C8   C9    aromatic  1.397  0.020  1.397
 CIU  C8   C13   aromatic  1.399  0.020  1.399
 CIU  I4   C11   single    2.103  0.020  2.103
 CIU  C9   C10   aromatic  1.388  0.020  1.388
 CIU  C9   H9    single    0.930  0.020  1.080
 CIU  C10  C11   aromatic  1.385  0.020  1.385
 CIU  C10  H10   single    0.930  0.020  1.080
 CIU  C11  C12   aromatic  1.387  0.020  1.387
 CIU  C12  C13   aromatic  1.383  0.020  1.383
 CIU  C12  H12   single    0.930  0.020  1.080
 CIU  C13  H13   single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 CIU  HC12  C1   HC11  106.38  3.000
 CIU  HC12  C1   C6    110.44  3.000
 CIU  HC11  C1   C6    109.44  3.000
 CIU  HC12  C1   C2    109.72  3.000
 CIU  HC11  C1   C2    109.28  3.000
 CIU  C6    C1   C2    111.45  3.000
 CIU  HC22  C2   HC21  106.85  3.000
 CIU  HC22  C2   C3    109.34  3.000
 CIU  HC21  C2   C3    109.63  3.000
 CIU  HC22  C2   C1    109.22  3.000
 CIU  HC21  C2   C1    110.60  3.000
 CIU  C3    C2   C1    111.11  3.000
 CIU  HC31  C3   N1    107.13  3.000
 CIU  HC31  C3   C4    108.43  3.000
 CIU  N1    C3   C4    112.16  3.000
 CIU  HC31  C3   C2    108.20  3.000
 CIU  N1    C3   C2    109.84  3.000
 CIU  C4    C3   C2    110.91  3.000
 CIU  HC42  C4   HC41  106.85  3.000
 CIU  HC42  C4   C5    110.43  3.000
 CIU  HC41  C4   C5    109.77  3.000
 CIU  HC42  C4   C3    109.60  3.000
 CIU  HC41  C4   C3    108.97  3.000
 CIU  C5    C4   C3    111.12  3.000
 CIU  HC52  C5   HC51  106.37  3.000
 CIU  HC52  C5   C6    110.43  3.000
 CIU  HC51  C5   C6    109.29  3.000
 CIU  HC52  C5   C4    110.00  3.000
 CIU  HC51  C5   C4    109.20  3.000
 CIU  C6    C5   C4    111.41  3.000
 CIU  HC62  C6   HC61  106.51  3.000
 CIU  HC62  C6   C5    109.33  3.000
 CIU  HC61  C6   C5    110.26  3.000
 CIU  HC62  C6   C1    109.31  3.000
 CIU  HC61  C6   C1    110.18  3.000
 CIU  C5    C6   C1    111.12  3.000
 CIU  HN1   N1   C7    119.46  3.000
 CIU  HN1   N1   C3    116.73  3.000
 CIU  C7    N1   C3    122.96  3.000
 CIU  N2    C7   O2    123.11  3.000
 CIU  N2    C7   N1    113.43  3.000
 CIU  O2    C7   N1    123.45  3.000
 CIU  HN2   N2   C8    114.66  3.000
 CIU  HN2   N2   C7    117.01  3.000
 CIU  C8    N2   C7    128.11  3.000
 CIU  C13   C8   C9    118.32  3.000
 CIU  C13   C8   N2    116.93  3.000
 CIU  C9    C8   N2    124.73  3.000
 CIU  H9    C9   C10   118.59  3.000
 CIU  H9    C9   C8    121.15  3.000
 CIU  C10   C9   C8    120.26  3.000
 CIU  H10   C10  C11   121.04  3.000
 CIU  H10   C10  C9    118.45  3.000
 CIU  C11   C10  C9    120.51  3.000
 CIU  C12   C11  C10   120.01  3.000
 CIU  C12   C11  I4    119.97  3.000
 CIU  C10   C11  I4    120.02  3.000
 CIU  H12   C12  C13   119.07  3.000
 CIU  H12   C12  C11   121.45  3.000
 CIU  C13   C12  C11   119.48  3.000
 CIU  H13   C13  C12   118.78  3.000
 CIU  H13   C13  C8    119.80  3.000
 CIU  C12   C13  C8    121.42  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 CIU  CONST_01  C11  C10  C9   C8     0.00   0.0  0
 CIU  CONST_02  C11  C12  C13  C8     0.00   0.0  0
 CIU  CONST_03  C12  C13  C8   C9     0.00   0.0  0
 CIU  CONST_04  C12  C11  C10  C9     0.00   0.0  0
 CIU  CONST_05  C13  C8   C9   C10    0.00   0.0  0
 CIU  CONST_06  C13  C12  C11  C10    0.00   0.0  0
 CIU  CONST_07  C10  C9   C8   N2   180.00   0.0  0
 CIU  CONST_08  C12  C13  C8   N2   180.00   0.0  0
 CIU  CONST_09  C9   C10  C11  I4   180.00   0.0  0
 CIU  CONST_10  C13  C12  C11  I4   180.00   0.0  0
 CIU  CONST_11  H10  C10  C9   C8   180.00   0.0  0
 CIU  CONST_12  H12  C12  C13  C8   180.00   0.0  0
 CIU  CONST_13  H13  C13  C8   C9   180.00   0.0  0
 CIU  CONST_14  H9   C9   C10  C11  180.00   0.0  0
 CIU  CONST_16  C13  C8   N2   C7   180.00   0.0  0
 CIU  CONST_17  HN2  N2   C8   C9   180.00   0.0  0
 CIU  CONST_18  O2   C7   N1   C3     0.00   0.0  0
 CIU  CONST_19  C8   N2   C7   O2     0.00   0.0  0
 CIU  CONST_20  C8   N2   C7   N1   180.00   0.0  0
 CIU  CONST_21  N2   C7   N1   C3   180.00   0.0  0
 CIU  CONST_22  HN1  N1   C7   O2   180.00   0.0  0
 CIU  Var_01    C4   C5   C6   C1   -55.09  30.0  1
 CIU  Var_02    C5   C6   C1   C2    55.16  30.0  1
 CIU  Var_03    C6   C1   C2   C3   -55.70  30.0  1
 CIU  Var_04    C6   C5   C4   C3    55.56  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 CIU  chir_01  C3  C2  C4  N1  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 CIU  plan-1  N2   0.020
 CIU  plan-1  C8   0.020
 CIU  plan-1  C9   0.020
 CIU  plan-1  C10  0.020
 CIU  plan-1  C11  0.020
 CIU  plan-1  C12  0.020
 CIU  plan-1  C13  0.020
 CIU  plan-1  H9   0.020
 CIU  plan-1  H10  0.020
 CIU  plan-1  H12  0.020
 CIU  plan-1  H13  0.020
 CIU  plan-1  I4   0.020
 CIU  plan-2  C3   0.020
 CIU  plan-2  N1   0.020
 CIU  plan-2  C7   0.020
 CIU  plan-2  O2   0.020
 CIU  plan-2  N2   0.020
 CIU  plan-2  C8   0.020
 CIU  plan-2  HN1  0.020
 CIU  plan-2  HN2  0.020

